Bio.Alphabet removed from Biopython

[maxdevblock]

import phylopandas as ph

raises error

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-12-ea858ee76df5> in <module>
----> 1 import phylopandas as ph

~/anaconda3/envs/covid/lib/python3.8/site-packages/phylopandas/__init__.py in <module>
     26 
     27 # Register PhyloPandas Methods
---> 28 from .core import PhyloPandasDataFrameMethods as _PhyloPandasDataFrameMethods
     29 from .core import PhyloPandasSeriesMethods as _PhyloPandasSeriesMethods
     30 from .seqio import *

~/anaconda3/envs/covid/lib/python3.8/site-packages/phylopandas/core.py in <module>
      3 from pandas_flavor import register_dataframe_accessor, register_series_accessor
      4 
----> 5 from . import seqio
      6 from . import treeio
      7 

~/anaconda3/envs/covid/lib/python3.8/site-packages/phylopandas/seqio/__init__.py in <module>
----> 1 from .read import (read_embl,
      2                    read_fasta,
      3                    read_fastq,
      4                    read_nexus_seq,
      5                    read_swiss,

~/anaconda3/envs/covid/lib/python3.8/site-packages/phylopandas/seqio/read.py in <module>
      8 from Bio.SeqRecord import SeqRecord
      9 from Bio.Blast import NCBIXML
---> 10 import Bio.Alphabet
     11 
     12 # Import Phylopandas DataFrame

~/anaconda3/envs/covid/lib/python3.8/site-packages/Bio/Alphabet/__init__.py in <module>
     18 """
     19 
---> 20 raise ImportError(
     21     "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
     22 )

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

[josesho]

bumping this, any workarounds?

[vectorvp]

Made a pull request to fix this #39

[simonjuleseric2]

Any news concerning this issue?

[Zymeth0211]

Yeah, I too have a problem with this issue yet unsolved that I could not import.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[2], [line 1](vscode-notebook-cell:?execution_count=2&line=1)
----> [1](vscode-notebook-cell:?execution_count=2&line=1) import phylopandas as ph

File [c:\Users\muham\AppData\Local\Programs\Python\Python312\Lib\site-packages\phylopandas\__init__.py:28](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/__init__.py:28)
     [25](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/__init__.py:25) from pandas import DataFrame
     [27](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/__init__.py:27) # Register PhyloPandas Methods
---> [28](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/__init__.py:28) from .core import PhyloPandasDataFrameMethods as _PhyloPandasDataFrameMethods
     [29](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/__init__.py:29) from .core import PhyloPandasSeriesMethods as _PhyloPandasSeriesMethods
     [30](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/__init__.py:30) from .seqio import *

File [c:\Users\muham\AppData\Local\Programs\Python\Python312\Lib\site-packages\phylopandas\core.py:5](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/core.py:5)
      [2](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/core.py:2) import pandas as pd
      [3](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/core.py:3) from pandas_flavor import register_dataframe_accessor, register_series_accessor
----> [5](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/core.py:5) from . import seqio
      [6](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/core.py:6) from . import treeio
      [9](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/core.py:9) try: 

File [c:\Users\muham\AppData\Local\Programs\Python\Python312\Lib\site-packages\phylopandas\seqio\__init__.py:1](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:1)
----> [1](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:1) from .read import (read_embl,
      [2](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:2)                    read_fasta,
      [3](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:3)                    read_fastq,
      [4](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:4)                    read_nexus_seq,
      [5](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:5)                    read_swiss,
      [6](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:6)                    read_phylip,
      [7](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:7)                    read_clustal,
      [8](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:8)                    read_blast_xml,
      [9](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:9)                    read_phylip_relaxed,
     [10](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:10)                    read_phylip_sequential)
     [12](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/__init__.py:12) from . import write

File [c:\Users\muham\AppData\Local\Programs\Python\Python312\Lib\site-packages\phylopandas\seqio\read.py:10](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/read.py:10)
      [8](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/read.py:8) from Bio.SeqRecord import SeqRecord
      [9](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/read.py:9) from Bio.Blast import NCBIXML
---> [10](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/read.py:10) import Bio.Alphabet
     [12](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/read.py:12) # Import Phylopandas DataFrame
     [13](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/phylopandas/seqio/read.py:13) import pandas as pd

File [c:\Users\muham\AppData\Local\Programs\Python\Python312\Lib\site-packages\Bio\Alphabet\__init__.py:20](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:20)
      [1](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:1) # Copyright 2000-2002 by Andrew Dalke.
      [2](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:2) # Revisions copyright 2007-2010 by Peter Cock.
      [3](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:3) # All rights reserved.
   (...)
      [7](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:7) # Please see the LICENSE file that should have been included as part of this
      [8](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:8) # package.
      [9](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:9) """Alphabets were previously used to declare sequence type and letters (OBSOLETE).
     [10](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:10) 
     [11](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:11) The design of Bio.Aphabet included a number of historic design choices
   (...)
     [17](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:17) transition from Bio.Alphabet to molecule type annotations.
     [18](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:18) """
---> [20](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:20) raise ImportError(
     [21](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:21)     "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
     [22](file:///C:/Users/muham/AppData/Local/Programs/Python/Python312/Lib/site-packages/Bio/Alphabet/__init__.py:22) )

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information

Would author @Zsailer help us regarding this problem?

Thank you